Cleft palate is among the most common birth defects in humans. In recent years, significant progress has been achieved in identifying genetic factors associated with cleft palate in humans. In addition, targeted mutagenesis studies in mice have found that mutations in a large number of genes each could cause cleft palate. However, little is known about how these genes are connected to form the molecular network controlling palate development. Recent advances in massively parallel sequencing technologies, in combination with chromatin immunoprecipitation (ChIP-seq) and gene expression profiling approaches, have enabled comprehensive analyses of genome-wide transcriptional regulation of gene expression in development and disease processes. In this proposal, we focus on characterizing the roles of two critical transcription factors, Osr2 and Pax9, in palate development. Mice lacking either Osr2 or Pax9 have complete cleft palate. Expression of both Osr2 and Pax9 mRNAs in the palatal mesenchyme is positively regulated by Fgf signaling. In addition, previous studies suggested that both Bmp and Fgf signaling pathways play critical roles in palate development and that Bmp signaling appeared to repress Pax9 gene expression in the anterior region of the developing palate. We propose three specific aims for this research project: (1) to characterize the roles of and the molecular pathway involving Osr2 in palate development using ChIP-seq and genome-scale gene expression profiling approaches in combination with mutant mouse studies; (2) to characterize the roles of and molecular pathway involving Pax9 in palate development and to investigate whether Osr2 and Pax9 interact directly and/or converge on regulation of downstream genes during palate development; and (3) to investigate the roles of the Bmp and Fgf signaling in molecular patterning of the secondary palate and whether Osr2 and Pax9 play critical roles in the integration of these signaling pathways in the regulation of palate development. These studies will not only significantly improve our understanding of the essential roles of Osr2 and Pax9 in palate development but also provide valuable resources and a transcriptional regulatory framework for comprehensive elucidation of the gene regulatory network controlling palate development.